Run black on package

Black is an autoformatter that has ensures that the formatted code
adheres to some strict guidelines. The formatted code should pass pylint
and flake8, so it will be an easy way to ensure consistent formatting
without having to deal with trial and error corrections to linters.

Author: kimt33

docs/conf.py

@@ -7,58 +7,58 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.doctest',
-    'sphinx.ext.todo',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.coverage',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.autosummary',
-    'sphinxcontrib.bibtex',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
+    "sphinx.ext.todo",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.coverage",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.autosummary",
+    "sphinxcontrib.bibtex",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 
 mathjax_path = "https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
 
 sphinx_gallery_conf = {
     # path to examples scripts
-    'examples_dirs': '../examples',
+    "examples_dirs": "../examples",
     # path where to save the generated examples
-    'gallery_dirs': 'auto_examples',
+    "gallery_dirs": "auto_examples",
     # path to the default thumb pics
     # 'default_thumb_file': './_static/wfns_white_bg_logo.png',
     # set the plot file pattern
-    'filename_pattern': '/(plot_.*|.*_plot.py$)',
+    "filename_pattern": "/(plot_.*|.*_plot.py$)",
 }
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The encoding of source files.
 # source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u'wfns'
-copyright = u'2017, Ayers\' Group @ McMaster University'
-author = u'Ayers\' Group @ McMaster University'
+project = u"wfns"
+copyright = u"2017, Ayers' Group @ McMaster University"
+author = u"Ayers' Group @ McMaster University"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = u'0.0.0'
+version = u"0.0.0"
 # The full version, including alpha/beta/rc tags.
-release = u'0.0'
+release = u"0.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -75,7 +75,7 @@
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build', '_themes/*', 'sphinxext']
+exclude_patterns = ["_build", "_themes/*", "sphinxext"]
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
@@ -93,7 +93,7 @@
 # show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
 # modindex_common_prefix = []
@@ -108,8 +108,8 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'sphinx_rtd_theme'
-html_theme_path = ["_themes/sphinx_rtd_theme/", ]
+html_theme = "sphinx_rtd_theme"
+html_theme_path = ["_themes/sphinx_rtd_theme/"]
 html_show_sourcelink = False
 
 # Theme options are theme-specific and customize the look and feel of a theme
@@ -134,12 +134,12 @@
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-html_favicon = '_static/wfns_favicon.ico'
+html_favicon = "_static/wfns_favicon.ico"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
@@ -202,30 +202,27 @@
 # html_search_scorer = 'scorer.js'
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'wfnsdoc'
+htmlhelp_basename = "wfnsdoc"
 
 # -- imgmath for equation generation --------------------------------------
 
 # imgmath_latex_preamble = r'''\usepackage{physics}'''
 
 # -- Options for LaTeX output ---------------------------------------------
 
-latex_engine = 'pdflatex'
+latex_engine = "pdflatex"
 
 latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
-    'papersize': 'letterpaper',
-
+    "papersize": "letterpaper",
     # The font size ('10pt', '11pt' or '12pt').
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
-    'preamble': r'''
+    "preamble": r"""
 \usepackage{amsmath}
 \usepackage{amsfont}
 \usepackage{braket}
-''',
-
+""",
     # Latex figure (float) alignment
     # 'figure_align': 'htbp',
 }
@@ -234,8 +231,13 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'wfns.tex', u'Project Documentation',
-     u'Ayers\' Group @ McMaster University', 'manual'),
+    (
+        master_doc,
+        "wfns.tex",
+        u"Project Documentation",
+        u"Ayers' Group @ McMaster University",
+        "manual",
+    )
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -263,10 +265,7 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'wfns', u'Project Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "wfns", u"Project Documentation", [author], 1)]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False
@@ -278,9 +277,15 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'wfns', u'Project Documentation',
-     author, 'wfns', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "wfns",
+        u"Project Documentation",
+        author,
+        "wfns",
+        "One line description of project.",
+        "Miscellaneous",
+    )
 ]
 
 # Documents to append as an appendix to all manuals.
@@ -300,12 +305,12 @@
 
 # Put class docstring and the __init__ docstring together in the documentation
 # for your class when you use the autoclass directive.
-autoclass_content = 'both'
+autoclass_content = "both"
 
-autodoc_member_order = 'bysource'
+autodoc_member_order = "bysource"
 # autodoc_default_flags = ['members', 'undoc-members', 'inherited-members', 'show-inheritance']
 
 # -----------------------------------------------------------------------------
 # Autosummary
 # -----------------------------------------------------------------------------
-autosummary_generate = ['tech_api.rst']
+autosummary_generate = ["tech_api.rst"]

scripts/horton_gaussian_fchk.py

@@ -44,7 +44,7 @@ def gaussian_fchk(fchk_file, horton_internal=False):
 
     # for spin orbitals
     exps = [mol.exp_alpha]
-    if hasattr(mol, 'exp_beta'):
+    if hasattr(mol, "exp_beta"):
         exps.append(mol.exp_beta)
 
     obasis = mol.obasis
@@ -64,10 +64,10 @@ def gaussian_fchk(fchk_file, horton_internal=False):
     for i, exp_i in enumerate(exps):
         for j, exp_j in enumerate(exps[i:]):
             j += i
-            temp = np.einsum('sd,pqrs->pqrd', exp_j.coeffs, two_ab, casting='no', order='C')
-            temp = np.einsum('rc,pqrd->pqcd', exp_i.coeffs, temp, casting='no', order='C')
-            temp = np.einsum('qb,pqcd->pbcd', exp_j.coeffs, temp, casting='no', order='C')
-            temp = np.einsum('pa,pbcd->abcd', exp_i.coeffs, temp, casting='no', order='C')
+            temp = np.einsum("sd,pqrs->pqrd", exp_j.coeffs, two_ab, casting="no", order="C")
+            temp = np.einsum("rc,pqrd->pqcd", exp_i.coeffs, temp, casting="no", order="C")
+            temp = np.einsum("qb,pqcd->pbcd", exp_j.coeffs, temp, casting="no", order="C")
+            temp = np.einsum("pa,pbcd->abcd", exp_i.coeffs, temp, casting="no", order="C")
             two_mo.append(temp)
         one_mo.append(exp_i.coeffs.T.dot(one_ab).dot(exp_i.coeffs))
 
@@ -78,8 +78,9 @@ def gaussian_fchk(fchk_file, horton_internal=False):
         "two_int": tuple(two_mo),
     }
     if horton_internal:
-        raise NotImplementedError('horton_internal storage is unsupported until it become Python '
-                                  '3.6 compatible.')
+        raise NotImplementedError(
+            "horton_internal storage is unsupported until it become Python " "3.6 compatible."
+        )
         # output["horton_internal"] = {
         #     "mol": mol,
         #     "lf": mol.lf,
@@ -90,20 +91,20 @@ def gaussian_fchk(fchk_file, horton_internal=False):
     return output
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     # extract keyword from command line
     kwargs = {key: val for key, val in zip(sys.argv[4::2], sys.argv[5::2])}
     # change data types
-    if 'horton_internal' in kwargs:
-        kwargs['horton_internal'] = (kwargs['horton_internal'] == 'True')
+    if "horton_internal" in kwargs:
+        kwargs["horton_internal"] = kwargs["horton_internal"] == "True"
 
     data = gaussian_fchk(**kwargs)
-    np.save(sys.argv[1], [data['el_energy'], data['nuc_nuc_energy']])
-    if len(data['one_int']) == 1:
-        np.save(sys.argv[2], data['one_int'][0])
+    np.save(sys.argv[1], [data["el_energy"], data["nuc_nuc_energy"]])
+    if len(data["one_int"]) == 1:
+        np.save(sys.argv[2], data["one_int"][0])
     else:
-        np.save(sys.argv[2], data['one_int'])
-    if len(data['two_int']) == 1:
-        np.save(sys.argv[3], data['two_int'][0])
+        np.save(sys.argv[2], data["one_int"])
+    if len(data["two_int"]) == 1:
+        np.save(sys.argv[3], data["two_int"][0])
     else:
-        np.save(sys.argv[3], data['two_int'])
+        np.save(sys.argv[3], data["two_int"])

scripts/horton_hartreefock.py

@@ -8,15 +8,32 @@
 """
 import sys
 import numpy as np
-from horton import (IOData, get_gobasis,
-                    PlainSCFSolver, EDIIS2SCFSolver,
-                    DenseLinalgFactory,
-                    compute_nucnuc, guess_core_hamiltonian, transform_integrals,
-                    AufbauOccModel, RTwoIndexTerm, RDirectTerm, RExchangeTerm, REffHam)
-
-
-def hartreefock(fn=None, basis=None, nelec=None, solver=EDIIS2SCFSolver, tol=1.0e-12,
-                horton_internal=False, **kwargs):
+from horton import (
+    IOData,
+    get_gobasis,
+    PlainSCFSolver,
+    EDIIS2SCFSolver,
+    DenseLinalgFactory,
+    compute_nucnuc,
+    guess_core_hamiltonian,
+    transform_integrals,
+    AufbauOccModel,
+    RTwoIndexTerm,
+    RDirectTerm,
+    RExchangeTerm,
+    REffHam,
+)
+
+
+def hartreefock(
+    fn=None,
+    basis=None,
+    nelec=None,
+    solver=EDIIS2SCFSolver,
+    tol=1.0e-12,
+    horton_internal=False,
+    **kwargs
+):
     """Run a HF calculation using HORTON.
 
     Parameters
@@ -101,7 +118,7 @@ def hartreefock(fn=None, basis=None, nelec=None, solver=EDIIS2SCFSolver, tol=1.0
         ham.compute_fock(fock_alpha)
         orb.from_fock_and_dm(fock_alpha, dm, olp)
     else:
-        raise ValueError('Given solver, {0}, is not callable'.format(solver))
+        raise ValueError("Given solver, {0}, is not callable".format(solver))
     energy = ham.cache["energy"]
 
     # Transform one- and two- electron integrals into MO basis
@@ -125,35 +142,36 @@ def hartreefock(fn=None, basis=None, nelec=None, solver=EDIIS2SCFSolver, tol=1.0
             "occ_model": occ_model,
             "one": one,
             "two": two,
-            "orb": [orb, ],
+            "orb": [orb],
             "olp": olp,
         }
-        raise NotImplementedError('horton_internal storage is unsupported until it become Python '
-                                  '3.6 compatible.')
+        raise NotImplementedError(
+            "horton_internal storage is unsupported until it become Python " "3.6 compatible."
+        )
 
     return output
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     # extract keyword from command line
     kwargs = {key: val for key, val in zip(sys.argv[4::2], sys.argv[5::2])}
     # change data types
-    if 'nelec' in kwargs:
-        kwargs['nelec'] = int(kwargs['nelec'])
-    if 'tol' in kwargs:
-        kwargs['tol'] = float(kwargs['tol'])
-    if 'horton_internal' in kwargs:
-        kwargs['horton_internal'] = bool(kwargs['horton_internal'])
-    if 'solver' in kwargs:
-        kwargs['solver'] = locals()[kwargs['solver']]
+    if "nelec" in kwargs:
+        kwargs["nelec"] = int(kwargs["nelec"])
+    if "tol" in kwargs:
+        kwargs["tol"] = float(kwargs["tol"])
+    if "horton_internal" in kwargs:
+        kwargs["horton_internal"] = bool(kwargs["horton_internal"])
+    if "solver" in kwargs:
+        kwargs["solver"] = locals()[kwargs["solver"]]
 
     data = hartreefock(**kwargs)
-    np.save(sys.argv[1], [data['el_energy'], data['nuc_nuc_energy']])
-    if len(data['one_int']) == 1:
-        np.save(sys.argv[2], data['one_int'][0])
+    np.save(sys.argv[1], [data["el_energy"], data["nuc_nuc_energy"]])
+    if len(data["one_int"]) == 1:
+        np.save(sys.argv[2], data["one_int"][0])
     else:
-        np.save(sys.argv[2], data['one_int'])
-    if len(data['two_int']) == 1:
-        np.save(sys.argv[3], data['two_int'][0])
+        np.save(sys.argv[2], data["one_int"])
+    if len(data["two_int"]) == 1:
+        np.save(sys.argv[3], data["two_int"][0])
     else:
-        np.save(sys.argv[3], data['two_int'])
+        np.save(sys.argv[3], data["two_int"])